Experiment: 5CCY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E5E	PDB entry 4E5E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.2 M magnesium chloride, 5 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.908	α = 90
b = 73.908	β = 90
c = 128.282	γ = 120

Symmetry
Space Group	P 64 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2014-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.1	64.006	100	0.119	0.121	0.022	6	28.4		12747

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	100		0.965	0.982	0.179	0.92		28.1	1243

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4E5E	2.1	50.01	12084	623	99.85	0.1747	0.1712	0.2438	RANDOM	37.181

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.47	-0.23		-0.47		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.495
r_dihedral_angle_4_deg	21.032
r_dihedral_angle_3_deg	15.914
r_dihedral_angle_1_deg	6.372
r_mcangle_it	3.295
r_mcbond_it	2.221
r_mcbond_other	2.216
r_angle_refined_deg	2.198
r_angle_other_deg	1.194
r_chiral_restr	0.162

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.495
r_dihedral_angle_4_deg	21.032
r_dihedral_angle_3_deg	15.914
r_dihedral_angle_1_deg	6.372
r_mcangle_it	3.295
r_mcbond_it	2.221
r_mcbond_other	2.216
r_angle_refined_deg	2.198
r_angle_other_deg	1.194
r_chiral_restr	0.162
r_bond_refined_d	0.025
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1458
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.